[BioC] org.Hs.eg question
Sim, Fraser
Fraser_Sim at URMC.Rochester.edu
Wed Mar 18 22:33:31 CET 2009
Hi,
I'm using the org.Hs.eg annotation package to convert Ensembl protein
annotations to Entrez GeneIds. I don't understand why although I can
find the correct annotation manually via the Ensembl website (EG =
4340), the annotation package is unable to.
Here is the code:
> HsENSP
[1] "ENSP00000373017"
> require("org.Hs.eg.db")
> HsEG = as.character(unlist(mget(HsENSP, org.Hs.egENSEMBLPROT2EG,
ifnotfound = NA)))
> HsEG
[1] NA
Thanks for any input.
Regards,
Fraser
> sessionInfo()
R version 2.8.1 (2008-12-22)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] gplots_2.6.0 gdata_2.4.2 gtools_2.5.0
[4] bioDist_1.14.0 RColorBrewer_1.0-2 GEOquery_2.6.0
[7] RCurl_0.94-0 rae230a.db_2.2.5 org.Rn.eg.db_2.2.6
[10] hom.Rn.inp.db_2.2.5 org.Hs.eg.db_2.2.6 RSQLite_0.7-1
[13] DBI_0.2-4 AnnotationDbi_1.4.2 Biobase_2.2.1
[16] rcom_2.0-4 rscproxy_1.0-12
>
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